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Hello,
I want to do some analysis with x3dna-v2.1. At first I met the problem: open_file </home/user/x3dna-v2.1/BASEPARS/misc_3dna.par> failed: No such file or directory, and I changed the directory name from config to BASEPARS. But another error came: error reading upper HB criteria/alternative indicator. I do not know how to solve it. Can anyone help me?
Beibei
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It seems your 3DNA setup is at fault. See the post "How to install 3DNA on Linux and Windows? (http://forum.x3dna.org/howtos/how-to-install-3dna-on-linux-and-windows/)" for more details.
What does the following commands give?
echo $X3DNA
find_pair -h
HTH,
Xiang-Jun
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Thank you! I figured out that.
But I still have another problem.
It says: more than one O5' atoms : residue name 'CYT', chain A, number *****the first atom is used*****
But in my pdb file, i just have one O5' atom. I use 5PHO patch for the 5' terminal, is the O5T atom identified as another O5' atom.
Beibei
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It's likely. Could you post an example?
Xiang-Jun
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I am attaching my input pdb file and the results I got.
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Thank for providing a sample PDB file which helps clarify the issue.
ATOM 5 O1P CYT A 1 17.752 35.775 26.807 1.00 1.70 N01A
ATOM 6 O2P CYT A 1 17.012 35.542 24.381 1.00 1.70 N01A
ATOM 7 O5' CYT A 1 18.906 34.140 25.293 1.00 1.77 N01A
ATOM 8 O5T CYT A 1 19.074 36.580 24.990 1.00 1.77 N01A
Yes, it is the O5T [8, atom serial number] which is taken as O5' by the 'analyze' program. Since the CYT #1 on chain A already has an O5' atom [7], that explains the message:
more than one O5' atoms : residue name 'CYT', chain A, number [ 1 ]
*****the first atom is used*****
In your case, the assumption of taking the 1st O5' atom [7] in calculations works fine.
Which software did you use? This is the first time I noticed such an O5T naming. Presumably, O5T [8] should be the O3' atom in the preceding (5') nt. Here O5' [7] could be named O5T, which 3DNA handles without any problem.
HTH,
Xiang-Jun
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Thanks for your careful checking!
This is a type of 5' terminal patch in CHARMM force field.
Beibei
Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids
Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University